It would be more accurate to say that GR was atheist toward the end of his life, the last several years.

The fact that there is a chapel on the Enterprise is easily explained away ...

That it is an actual chapel would likely be the most straight forward explanation.

Yes, there was one. Hard to prove that Roddenberry didn't agree with it, unless someone has an actual record about his opinion on it.
Although it is very easily to imagine, that a TV show, a 60s sci-fi program of all things, has a very hard time generating ratings.
They try to appeal to a mostly christian audience, I think this much is undisputed.

So a TV Exec at the time reads the draft, reads the wedding scene in Balance of Terror and schedules the stage prop guys to produce a starship chapel, because it doesn't even occur to him that it might be a future without organized religion.
Seriously, a christian TV Exec who wants to sell his show to a 90% christian audience (presumably) would NOT imagine it any other way.
The second an atheist Roddenberry found out about it, he might protest, but a schedule to build the set has already been issued and the Exec would put the idea of no christianity in the future down anyway, cause he doesn't want to risk losing what scarce viewers they have.

Entirely speculated on my part, but given what I know about the time and circumstances very likely.

The gist of it is, apparently prayers only ever appear to have any effect at all, when the circumstances are ambiguous enough to allow a statistical glitch which then get's called a miracle.
For example 500 cancer patients praying to be cured. then a few of them indeed get healthy again. of course obviously God did it, never mind the scientifically sound methods of chemo, whatever other cancer treatments modern medicine has come up by now or even your own immune system fighting the cancer of and it going into remission.
As soon as any ambiguity is gone, like an amputee praying to jesus/god/allah/flyingspagetthimonster to restore his lost limb, the net result is always zero.
Apparently god hates amputees, because he never heals them.

Of course, I now fully expect any of the following rationalizations to debate this:

Healing amputees violates god's mysterious plan (even though cancer healing is allowed).
God needs to be hidden, healing an amputee would be to obvious a miracle (tell that to Jesus running around healing all sorts of people and resurrecting Lazarus from the dead).
God needs amputees to teach us all some obscure valueable lesson (why amputees and what are we supposed to learn from it if the message remains hidden).
It was the amputee's own choice to go into war and get his leg blown off. free will issue (tell that to an innocent kid after playing on a landmine field).
You are not allowed to test God with such an unreasonable prayer (then what are all the other prayers?)

Seriously, read the website and think 2 seconds about the whole issue... humor me, if you actually think prayers are anything other than useless superstition.